Fixes for deps.js and adjustments for no-dep build

Fix the module issue for the deps.js files by only running the shim transform on the files where we don't want the dependencies, adding the add-on requires back into main.js, and the removing the extraneous require() statements from the deps.js browserify build.

This introduced the problem of dealing with the add-on require statements in the situation where we don't want the dependencies (here they are added on after the browserify bundle process). I "fixed" this by shimming them out to the CodeMirror global, which we know will be there.

There has got to be a better way to do this.

That said, it the index.html file now seems to be serving properly and the yasqe.min.js file is working fine in Palladio where the jQuery, CodeMirror, and store globals are provided on the window object.